|
Status |
Public on Apr 15, 2012 |
Title |
C2.20wks |
Sample type |
SRA |
|
|
Source name |
3'-Seq in control mouse #2; age of 20 weeks
|
Organism |
Mus musculus |
Characteristics |
strain: FvB tissue: muscle age: 20 weeks
|
Extracted molecule |
polyA RNA |
Extraction protocol |
Total RNA was extracted from muscle tissue of either 20 weeks or 12 months old mice (either control mice or OPMD mice). mRNA was isolated, heat fragmented and the fragmented mRNA was then converted to single-stranded cDNA using SuperScript III reverse transcriptase and P7-t25-vn oligo-dT primer. This was followed by second-strand cDNA synthesis and end-repair using T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase. After purification, a P5-splinkerette was ligated and the splikerette-ligated cDNA was size-selected for approximately 220 bp long cDNA fragments using the E-Gel iBase Power System from Invitrogen. The final 3'Seq libraries were then generated by PCR amplification of the linker-ligated cDNA with P5 and P7 primers. After a last purification step the 3'Seq libraries were sequenced on the HiSeq systems. The 3 trePABPN1.A17 20-weeks old mice samples were indexed, pooled and sequenced together in one lane. Same is true for the 3 control 20-weeks old samples.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
3'-Seq in control mouse #2; age of 20 weeks
|
Data processing |
Reads were aligned to the mouse genome (mm9) using bowtie.
|
|
|
Submission date |
Sep 22, 2011 |
Last update date |
May 15, 2019 |
Contact name |
Ran Elkon |
Organization name |
Tel Aviv University
|
Department |
Human Genetics
|
Street address |
Ramat Aviv
|
City |
Tel Aviv |
ZIP/Postal code |
69494 |
Country |
Israel |
|
|
Platform ID |
GPL13112 |
Series (2) |
GSE32302 |
Genome-wide maps of polyadenylation sites in OPMD-model and control mice |
GSE32303 |
PABPN1 role in regulation of alternative cleavage and polyadenylation |
|
Relations |
SRA |
SRX099203 |
BioSample |
SAMN00727936 |